Australia's waters have been ranked as being the most biologically diverse in the world, yet up to 80 per cent of the species in it have yet to be discovered, a new study has shown.

In one of the final studies of the International Census of Marine Life, a survey of Australian waters has revealed it contains 32,889 known species, just pipping Japan with 32,777 known species.

The authors also estimate another 17,000-odd named species are also believed to occur in Australian waters, but have yet to be included in databases.

The findings appear in a series of papers published today in PLoS One, in the lead-up to the close of the 10-year census due on October 4.

Involving more than 2,000 scientists from more than 80 nations, the census is one of the largest global scientific collaborations yet undertaken, according to organisers.

Australian study lead author Dr Alan Butler, of CSIRO Marine and Atmospheric Research, says the survey of Australia's marine jurisdictional area, included offshore and sub-Antarctic islands and stretched to the tropical waters of the north.

The 9 million square kilometre zone includes 36,000 kilometres of coastline, 12,000 islands and spans 5000 kilometres from temperate to tropical latitudes.

"This constitutes a vast array of highly diverse habitats and ocean features; many have received limited, if any, exploration," Dr Butler and colleagues write.

'Needle in a haystack'

Dr Butler says trying to determine exactly what lies beneath Australia's territorial waters is akin to "finding a needle in a haystack".

He says although technology is improving researchers will probably never document every piece of ocean life.

"Imagine trying to study the flora and fauna of the Blue Mountains by flying over it in a helicopter in the dark with a hook on a line hanging down; it's a needle in a haystack."

Dr Butler and colleagues "crudely estimate" about 250,000 species of marine life in Australian waters currently remain unknown.

He says this figure is based on the findings of fieldwork that shows "whenever we do sampling about 80 per cent of what we find is new".

The paper draws upon field work and databases of the Australian Faunal Directory, Codes for Australian Aquatic Biota, Online Zoological Collections of Australian Museums, and the Australian node of the Ocean Biogeographic Information System to come to its conclusions.

Dr Butler says most of the known species live above two kilometres down in the ocean, with the vast majority of explored areas along the shallower waters of the continental shelf.

He says the deepest ocean that has been surveyed is four kilometres deep, using equipment borrowed from the United States. The greatest depth in Australian waters lies between five kilometres and six kilometres.

Marine diversity

In the Australian study, the largest group of known species is the mollusc family, with 8,525 species. But Dr Butler says this might not reflect the relative percentage of molluscs in Australia's oceans.

"We may have a lot of molluscs known because we had a good expertise in the field," he said.

The study identified 5,184 species of fish, and although the Great Barrier Reef has been widely studied, Dr Butler says new species of fish are still being found.

The survey shows most of Australia's endemic sea life lives in the south and has evolved since the split with Gondawana about 80 million years ago, says Dr Butler.

The north is a major "biodiversity hotspot" with a vast number of species that are common to south-east Asian waters.

Dr Butler says although the paper shows a challenge remains, he hopes it "heightens the feeling that we should look after what we have".

"We are custodians of a huge zone with a huge number of species," he said, adding that it is important to protect "whole systems" rather than single species.

"More and more the evidence shows [that] if you replace a jungle with a wheat field you make it impoverished and more vulnerable to collapse."